Prognostic and immunological role of cuproptosis-related protein FDX1 in pan-cancer

Article Biochemistry & Molecular Biology

Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning

Jialiang Yang et al.

Summary: By integrating deep learning models with H&E images and clinical information, accurate prediction of relapse and metastasis risk in HER2-positive breast cancer patients can be achieved.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

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Article Biochemical Research Methods

Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network

Zixuan Ye et al.

Summary: This paper proposes a method based on deep learning and random forest to predict the risk of metastasis and recurrence in cervical cancer whole slide H&E images. The experimental results show that high-level features extracted by deep convolutional neural network can effectively predict the risk of metastasis and recurrence.

CURRENT BIOINFORMATICS (2022)

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Article Genetics & Heredity

Reduced Immunogenicity of Intraparenchymal Delivery of Adeno-Associated Virus Serotype 2 Vectors: Brief Overview

Wuh-Liang Hwu et al.

Summary: This article illustrates the low risk of immune response to AAV serotype 2 vector-mediated gene therapy to the brain with support from clinical trial data in aromatic L-amino acid decarboxylase deficiency and Parkinson disease.

CURRENT GENE THERAPY (2022)

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Article Multidisciplinary Sciences

Copper induces cell death by targeting lipoylated TCA cycle proteins

Peter Tsvetkov et al.

Summary: Copper is an essential cofactor for all organisms, but excessive copper can lead to cell death. We found that copper-dependent cell death mechanism is different from known mechanisms, and it is related to mitochondrial respiration. Copper directly binds to lipoylated components of the tricarboxylic acid cycle, causing protein aggregation and loss of iron-sulfur cluster proteins, ultimately leading to cell death.

SCIENCE (2022)

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Article Oncology

A Systematic Framework for Identifying Prognostic Genes in the Tumor Microenvironment of Colon Cancer

Jinyang Liu et al.

Summary: This study investigated prognostic genes in the tumor microenvironment of colon cancer and found that stromal and immune scores were significantly associated with colon cancer stages. Through analysis of differentially expressed genes, 952 common DEGs were identified, which were associated with T-cell activation, immune receptor activity, and cytokine-cytokine receptor interaction. Univariate Cox regression identified 22 prognostic genes, and LASSO Cox regression identified 9 key prognostic genes. A prognostic model based on these 9 genes effectively predicted the outcome of colon cancer patients.

FRONTIERS IN ONCOLOGY (2022)

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Article Biology

Predicting breast cancer recurrence and metastasis risk by integrating color and texture features of histopathological images and machine learning technologies

Xinyu Liu et al.

Summary: In this study, a framework for assessing the risk of breast cancer recurrence and metastasis was developed using image features and machine learning technologies. The framework performed well on clinical data and an external validation dataset, and identified two important predictors.

COMPUTERS IN BIOLOGY AND MEDICINE (2022)

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Review Oncology

Connecting copper and cancer: from transition metal signalling to metalloplasia

Eva J. Ge et al.

Summary: Copper is a essential nutrient with both beneficial and toxic properties to cells. Recent progress in transition metal signaling has led to new connections between researchers from different disciplines, with potential for translating basic research into clinical therapies for diseases. The relationship between copper and cancer is particularly important, with opportunities for leveraging disease vulnerabilities through copper-dependent signaling pathways.

NATURE REVIEWS CANCER (2022)

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Review Biochemistry & Molecular Biology

Copper metabolism as a unique vulnerability in cancer

Vinit C. Shanbhag et al.

Summary: Over the past 25 years, significant progress has been made in identifying and characterizing proteins that regulate the uptake, intracellular trafficking and export of copper. While copper is essential for growth and development in humans and other mammals, it is also a limiting nutrient for cancer cell growth and proliferation. Oral copper chelators have been shown to have anti-neoplastic and anti-metastatic effects in animals and humans.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2021)

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Article Biochemical Research Methods

Deep-DRM: a computational method for identifying disease-related metabolites based on graph deep learning approaches

Tianyi Zhao et al.

Summary: This study introduces a graph deep learning method, Deep-DRM, for identifying diseases-related metabolites. By calculating the similarities between metabolites and diseases, building networks, and applying a deep neural network, Deep-DRM shows outstanding performance in identifying true metabolite-disease pairs.

BRIEFINGS IN BIOINFORMATICS (2021)

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Article Oncology

Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

Hyuna Sung et al.

Summary: The global cancer burden in 2020 saw an estimated 19.3 million new cancer cases and almost 10.0 million cancer deaths. Female breast cancer surpassed lung cancer as the most commonly diagnosed cancer, while lung cancer remained the leading cause of cancer death. These trends are expected to rise in 2040, with transitioning countries experiencing a larger increase compared to transitioned countries due to demographic changes and risk factors associated with globalization and a growing economy. Efforts to improve cancer prevention measures and provision of cancer care in transitioning countries will be crucial for global cancer control.

CA-A CANCER JOURNAL FOR CLINICIANS (2021)

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Article Biochemistry & Molecular Biology

Zic Family Member 2 (ZIC2): a Potential Diagnostic and Prognostic Biomarker for Pan-Cancer

Zhengtong Lv et al.

Summary: ZIC2 expression is commonly elevated in various cancers, and high ZIC2 expression is associated with worsened prognosis and higher clinicopathologic stage. ZIC2 expression is strongly correlated with TMB, MSI, tumor microenvironment, and tumor- and immune-related genes.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Pharmacology & Pharmacy

FDX1 can Impact the Prognosis and Mediate the Metabolism of Lung Adenocarcinoma

Zeyu Zhang et al.

Summary: This study constructed a risk signature related to LUAD using RNA-sequencing data and the LASSO algorithm, demonstrating that the risk signature is an independent risk factor for LUAD patients. Specifically focusing on the FDX1 gene, it was found that FDX1 promotes ATP production and is closely related to glucose metabolism, fatty acid oxidation, and amino acid metabolism.

FRONTIERS IN PHARMACOLOGY (2021)

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Article Cell Biology

Evaluating DNA Methylation, Gene Expression, Somatic Mutation, and Their Combinations in Inferring Tumor Tissue-of-Origin

Haiyan Liu et al.

Summary: Carcinoma of unknown primary (CUP) is a metastatic cancer with unidentified primary tumor site, affecting 5% of cancer cases in the US. Recent studies propose integrating machine learning techniques with diverse biomarkers to predict TOO, as traditional methods are limited in accurately identifying tissue-of-origin in CUP patients.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

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Review Biochemistry & Molecular Biology

Role of Copper on Mitochondrial Function and Metabolism

Lina M. Ruiz et al.

Summary: Copper is crucial for various life processes such as energy metabolism and oxidative stress management in eukaryotic organisms. Dysregulation of copper levels can lead to diseases like anemia and cancer, prompting research into potential therapeutic interventions targeting copper metabolism. This review explores the role of copper in cellular function, metabolic reprogramming, and cancer biology, highlighting its importance in the field of regenerative medicine and oncology.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Review Medicine, General & Internal

Tumor Microenvironment

Borros Arneth

MEDICINA-LITHUANIA (2020)

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Article Oncology

HLA-corrected tumor mutation burden and homologous recombination de fi ciency for the prediction of response to PD -(L)1 blockade in advanced non -small -cell lung cancer patients

J. H. Shim et al.

ANNALS OF ONCOLOGY (2020)

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Article Biotechnology & Applied Microbiology

TOOme: A Novel Computational Framework to Infer Cancer Tissue-of-Origin by Integrating Both Gene Mutation and Expression

Binsheng He et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

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Article Pathology

Association of serine/threonine kinase 11 mutations and response to programmed cell death 1 inhibitors in metastatic gastric cancer

Minsuk Kwon et al.

PATHOLOGY RESEARCH AND PRACTICE (2020)

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Article Biochemistry & Molecular Biology

A machine learning framework to trace tumor tissue-of-origin of 13 types of cancer based on DNA somatic mutation

Bingsheng He et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2020)

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Article Genetics & Heredity

miRNA-146a Improves Immunomodulatory Effects of MSC-derived Exosomes in Rheumatoid Arthritis

Fataneh Tavasolian et al.

CURRENT GENE THERAPY (2020)

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Article Biochemistry & Molecular Biology

Mitochondrial metabolism promotes adaptation to proteotoxic stress

Peter Tsvetkov et al.

NATURE CHEMICAL BIOLOGY (2019)

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Review Oncology

The Tumor Microenvironment Innately Modulates Cancer Progression

Dominique C. Hinshaw et al.

CANCER RESEARCH (2019)

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Editorial Material Biochemistry & Molecular Biology

SnapShot: TCGA-Analyzed Tumors

Amy Blum et al.

CELL (2018)

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Review Biochemistry & Molecular Biology

Tumor microenvironment participates in metastasis of pancreatic cancer

Bo Ren et al.

MOLECULAR CANCER (2018)

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Article Multidisciplinary Sciences

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

Sanjeev Mariathasan et al.

NATURE (2018)

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Article Biochemistry & Molecular Biology

Changes in the Serum Levels of Trace Elements Before and After the Operation in Thyroid Cancer Patients

Abdulkerim Kasim Baltaci et al.

BIOLOGICAL TRACE ELEMENT RESEARCH (2017)

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Article Oncology

Nivolumab in patients with metastatic DNA mismatch repair-deficient or microsatellite instability-high colorectal cancer (CheckMate 142): an open-label, multicentre, phase 2 study

Michael J. Overman et al.

LANCET ONCOLOGY (2017)

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Article Biotechnology & Applied Microbiology

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells

Jialiang Yang et al.

BMC GENOMICS (2017)

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Article Oncology

Pre-diagnostic copper and zinc biomarkers and colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition cohort

Magdalena Stepien et al.

CARCINOGENESIS (2017)

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Review Biochemical Research Methods

Impact of the physical microenvironment on tumor progression and metastasis

Fabian Spill et al.

CURRENT OPINION IN BIOTECHNOLOGY (2016)

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Article Biotechnology & Applied Microbiology

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

Bo Li et al.

GENOME BIOLOGY (2016)

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Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

Katarzyna Tomczak et al.

Wspolczesna Onkologia-Contemporary Oncology (2015)

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Article Multidisciplinary Sciences

Inferring tumour purity and stromal and immune cell admixture from expression data

Kosuke Yoshihara et al.

NATURE COMMUNICATIONS (2013)

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Article Oncology

Tumor-Infiltrating Lymphocyte Grade Is an Independent Predictor of Sentinel Lymph Node Status and Survival in Patients With Cutaneous Melanoma

Farhad Azimi et al.

JOURNAL OF CLINICAL ONCOLOGY (2012)

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Article Multidisciplinary Sciences

Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system

Natallia Strushkevich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

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Article Multidisciplinary Sciences

International network of cancer genome projects

Thomas J. Hudson et al.

NATURE (2010)

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Article Multidisciplinary Sciences

Humans possess two mitochondrial ferredoxins, Fdx1 and Fdx2, with distinct roles in steroidogenesis, heme, and Fe/S cluster biosynthesis

Alex D. Sheftel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

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Prognostic and immunological role of cuproptosis-related protein FDX1 in pan-cancer

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